JPAN! I have a HUGE problem!!
It appears that the RAM address you specified (0x0203E000) is used by the D/N system!!
What would be a good RAM address to use instead? (This is using BPEE)
EDIT: Also, the RAM address I changed it to doesn't seem to get refreshed upon starting a new game, with a game already having been saved!

Well, 0x0203e000 is the start, but in Emerald, all up to 0x0203ffff seems free. So, just choose 0x1000 area or Ram from where the D/N lets up and use that.
Also, Emerald appears to load Flash-to-RAM only once, at the start of the first screen. Previously unused areas of the RAM shouldn't be deleted by themselves on New Game. So, use a script that only happens on the new game (set by one of the old 0x40xx variables, that the game clears for you) that clears the entire memory area for you.